Laboratory for Phyloinformatics

Unit Leader

Shigehiro KurakuPh.D.

  • Location:Kobe / Developmental Biology Buildings
  • E-mail:shigehiro.kuraku[at]riken.jpPlease replace [at] with @.
  • Lab Website

Genome-wide scope and concepts of molecular evolution for entire life science

Research Area

The ‘genome’ stands for a complete set of genetic information per species (or cell) that is a blueprint of our body structure and biological processes at different levels. The genome was not suddenly created but is an interim product of successive modifications over billion years. Every single genome has a history embedded in DNA sequences, and comparisons of the information between species provide clues for past evolutionary events.

By making use of cutting-edge DNA sequencing technologies and bioinformatics, we conduct molecular-level analysis on diversity and evolution of genomes and epigenomes of vertebrates. Our activity includes taking an initiative in whole genome sequencing and analysis projects for some important vertebrate species, which is leading to our fostering of biodiversity literacy from viewpoints of genomics and molecular evolution.

Research Theme

  • Biodiversity research based on understanding of life sciences and molecular evolutionary approaches
  • Improvement of genome analysis techniques for chromosome-scale DNA sequencing
  • Vertebrate evolutionary genomics encompassing chromatin organization and regulation
  • Decoding genomes of important organisms with little molecular information

Main Publications List

  • Onimaru K, Motone F, Kiyatake I, et al.
    A staging table for the embryonic development of the brownbanded bamboo shark(Chiloscyllium punctatum).
    Developmental Dynamics (2018) doi :10.1002/dvdy.24623
  • Nishimura O, Hara Y, Kuraku S.
    gVolante for standardizing completeness assessment of genome and transcriptome assemblies.
    Bioinformatics 33(22). 3635–3637 (2017) doi: 10.1093/bioinformatics/btx445
  • Kadota M, Hara Y, Tanaka K, et al.
    CTCF binding landscape in jawless fish with reference to Hox cluster evolution.
    Scientific Reports 7(1). 4957 (2017) doi: 10.1038/s41598-017-04506-x
  • Onimaru K, Kuraku S.
    Inference of the ancestral vertebrate phenotype through vestiges of the whole genome duplications
    Briefings in Functional Genomics (2018) doi: 10.1093/bfgp/ely008
  • Kuraku S, Feiner N, Keeley SD, Hara Y.
    Incorporating tree-thinking and evolutionary time scale into developmental biology.
    Development, Growth & Differentiation 58(1). 131-42 (2016) doi: 10.1111/dgd.12258
  • Hara Y, Tatsumi K, Yoshida M, et al.
    Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation
    BMC Genomics 16. 977 (2015) doi: 10.1186/s12864-015-2007-1
  • Tatsumi K, Nishimura O, Itomi K, et al.
    Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing.
    Biotechniques 58(5). 253-257 (2015) doi: 10.2144/000114288
  • Kuraku S, Zmasek CM, Nishimura O, Kato K.
    aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.
    Nucleic Acids Research 41. W22-28 (2013) doi: 10.1093/nar/gkt389
  • Smith JJ, Kuraku S, Holt C, et al.
    Sequencing of the sea lamprey (Petromyzon marinus ) genome provide insights into vertebrate evolution.
    Nature Genetics 45(4). 415-421 (2013) doi: 10.1038/ng.2568
  • Kuraku S.
    Impact of asymmetric gene repertoire between cyclostomes and gnathostomes.
    Seminars in Cell and Developmental Biology 24(2). 119-127 (2013) doi: 10.1016/j.semcdb.2012.12.009

Member

Shigehiro KurakuUnit Leader shigehiro.kuraku[at]riken.jp CV
Mitsutaka KadotaSenior Technical Scientis mitsutaka.kadota[at]riken.jp CV
Osamu NishimuraTechnical Scientist osamu.nishimura[at]riken.jp CV
Reiko NakagawaResearch Specialist reiko.nakagawa[at]riken.jp
Yuichiro HaraSpecial Postdoctoral Researcher yuichiro.hara[at]riken.jp CV
Koh OnimaruSpecial Postdoctoral Researcher koh.onimaru[at]riken.jp CV
Yoshinobu UnoResearch Scientist yoshinobu.uno[at]riken.jp CV
Kazuaki YamaguchiResearch Scientist kazuaki.yamaguchi[at]riken.jp CV
Rehab Fouad AbdelhamidTechnical Staff I
Chiharu TanegashimaTechnical Staff II chiharu.tanegashima[at]riken.jp
Kaori TatsumiTechnical Staff II

*:concurrent / Please replace [at] with @.